By application of the continuous optical scanning to polyacrylamide gel electrophoresis (PAGE), we have been able to 1) estimate the apparent diffusion coefficient (D') of a single protein in gel, and 2) empirically formulate the relationships between D' and a set of physical parameters such as current density, protein load, gel concentrations and ionic strength. The method has been further extended to study 1) the electrophoretic properties of micelles formed by sodium dodecyl sulfate (SDS) and lithium dodecyl sulfate (LDS), 2) the separation and characterization of protein-pigment complexes by SDS-PAGE using a mixture of ragweed pollen antigen as a model compound, and 3) the physical properties associated with agarose gel electrophoresis. Electrophoresis in polyacrylamide was compared with that in agarose gel under identical experimental conditions. Model compounds used for investigation are the peptide, adrenocorticotropic hormone (ACTH), and the protein mixture of ragweed pollen antigens.